Class: Utility::PcrCyclesBinningCalculator

Inherits:
Object
  • Object
show all
Includes:
ActiveModel::Model, CommonDilutionCalculations
Defined in:
app/models/utility/pcr_cycles_binning_calculator.rb

Overview

Handles the Computations for PCR Cycles binning. Used by the PCR Cycles Binned Plate class to handle the binning processing.

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(well_details) ⇒ PcrCyclesBinningCalculator

Returns a new instance of PcrCyclesBinningCalculator.



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# File 'app/models/utility/pcr_cycles_binning_calculator.rb', line 10

def initialize(well_details)
  @well_details = well_details
end

Instance Attribute Details

#config ⇒ Object (readonly) Originally defined in module CommonDilutionCalculations

Returns the value of attribute config.

Instance Method Details

#compute_presenter_bin_details ⇒ Object 



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# File 'app/models/utility/pcr_cycles_binning_calculator.rb', line 32

def compute_presenter_bin_details
  @well_details.each_with_object({}) do |(well_locn, well_detail), bin_dets|
    presenter_bins_key.each do |bin|
      next unless well_detail['pcr_cycles'] == bin['pcr_cycles']

      bin_dets[well_locn] = { 'colour' => bin['colour'], 'pcr_cycles' => bin['pcr_cycles'] }
    end
  end
end

#compute_vol_source_reqd(sample_conc) ⇒ float Originally defined in module CommonDilutionCalculations

Computes the volume of source material required for normalisation based on the sample concentration and attributes from the purpose configuration (target amount and volume, minimum source volume). Includes checks for minimum source volume and rounding for low diluent volumes due to liquid handler robot restrictions.

Parameters:

  • sample_conc (float) —

    The concentration of the source sample in ng/ul

Returns:

  • (float) —

    The volume of the source required in ul.

#compute_well_transfers(parent_plate) ⇒ Object 



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# File 'app/models/utility/pcr_cycles_binning_calculator.rb', line 14

def compute_well_transfers(parent_plate)
  bins_hash = pcr_cycle_bins
  compression_reqd = compression_required?(bins_hash, parent_plate.number_of_rows, parent_plate.number_of_columns)
  build_transfers_hash(bins_hash, parent_plate.number_of_rows, compression_reqd)
end

#construct_dest_qc_assay_attributes(child_uuid, transfer_hash) ⇒ array Originally defined in module CommonDilutionCalculations

Constructs the qc_assays collection details for use when writing calculated concentrations for the newly created child plate.

Parameters:

  • child_uuid (string) —

    The uuid of the child plate being transferred into.

  • transfer_hash (hash) —

    The transfers hash from which we extract the destination concentrations.

Returns:

  • (array) —

    An array of qc assay details for the child plate, ready to send via Api to sequencescape.

#extract_destination_concentrations(transfer_hash) ⇒ hash Originally defined in module CommonDilutionCalculations

Refactor the transfers hash to give destination concentrations

Parameters:

  • transfer_hash (hash) —

    The transfer details.

Returns:

  • (hash) —

    A refactored hash of well concentrations.

#normalisation_details(wells) ⇒ hash Originally defined in module CommonDilutionCalculations

Creates a hash of well normalisation details for a plate used when generating the well transfers and qc assays.

Parameters:

  • wells (Wells) —

    The source wells being normalised.

Returns:

  • (hash) —

    The well details hash containing calculated normalisation values.

#presenter_bins_key ⇒ Object 



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# File 'app/models/utility/pcr_cycles_binning_calculator.rb', line 20

def presenter_bins_key
  # fetch the array of bins as pcr cycles e.g. [16,14,12]
  bins = calculate_bins

  # dynamic number of bins so count the colours up from 1
  colour_index = 1
  bins.each_with_object([]) do |bin, templates|
    templates << { 'colour' => colour_index, 'pcr_cycles' => bin }
    colour_index += 1
  end
end